Microbial diversity and peptide dynamics during the spontaneous fermentation of whey from the Yunnan ethnic cheese Rushan

Rushan whey (RW) is a byproduct generated during Rushan cheese production. To evaluate the potential of RW as a source of bioactive peptides, the dynamics of indigenous microbial communities and peptide profiles were monitored throughout natural fermentation. Bacterial diversity dropped sharply within the first week of the 14‑day fermentation, whereas fungi were only detected at the end. Peptide diversity decreased over time, with peptides derived from β-casein consistently comprising the greatest share. The abundance of total peptides and bioactive peptides peaked on day 11, followed by a pronounced decline. Among the detected peptides, 19 were annotated as putative bioactive peptides. Additionally, variations in the abundance of total peptides, peptides derived from different casein fractions, and specific bioactive peptides were associated with the abundance of particular bacterial species. Overall, this study provides a scientific basis for enriching bioactive peptides in fermented RW through targeted inoculation with selected microbial starters.